Projects tagged ‘bio-informatics’ and ‘chemistry’

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame ... [More] files and computed normal modes from quantum programs. [Less]

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular ... [More] modeling, chemistry, solid-state materials, biochemistry, or related areas. [Less]

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search ... [More] , SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more. [Less]

JChemPaint is a program for drawing 2D chemical structures like those found in most chemistry textbooks.

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application ... [More] , is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. [Less]

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilities through OpenGL shaders to offers an array of innovative visual ... [More] effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins. * Real Time Ambient Occlusion * Depth Aware Silhouette Enhancement * Ball and Sticks, Space-Fill and Liquorice visualization modes * High resolution antialiased snapshots for creating publication quality renderings * Automatic generation of animated gifs of rotating molecules for web pages animations * Interactive rendering of large molecules and protein (>100k atoms) * Standard PDB input [Less]

The BinBase Database system was created to provide an accurate and fast solution for the analysis of thousand of Chromatograms and to create a library of compounds. Better known as Bins. The system ... [More] is so designed that it can be easily extended and adapted for your specific problems. You also have the possibilities to use it in different runtime configurations like: * using it as standalone system * using it with a cluster * using it with setupX as meta information provider * using with a custom meta information provider BinBase core part is now available in the svn. Websites are down to server error and we are working on it! [Less]

A collection of cheminformatics and machine-learning software written in C++ and Python.